Gram staining method with improved decolorization of the crystal violet-iodine complex from gram negative bacteria

ABSTRACT

Provided herein are methods of staining biological material for the purpose of detecting, and in some examples also identifying, microorganisms. Methods of Gram staining bacteria using a slow-acting decolorizing formulation, such as one that includes 1,2-propandiol or ethylene glycol, can be used to extend the time of the decolorizing step, and thus permit automation of the Gram staining method. Also provided are compositions and kits for performing automated Gram staining on microscope slides.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.13/773,864 filed Feb. 22, 2013, which claims priority to U.S.Provisional Application No. 61/612,520 filed Mar. 19, 2012, bothapplications herein incorporated by reference.

FIELD

The present disclosure relates to methods of staining biologicalmaterial for the purpose of detecting, and in some examples alsoidentifying, microorganisms. More particularly, the present disclosurerelates to methods, compositions, and kits for performing automated Gramstaining on microscope slides.

BACKGROUND

The Gram stain is a well-known, commonly used microbiological techniquefor the detection, classification, and identification of microorganisms,especially bacteria. The most common method of the Gram staininginvolves four steps: staining, trapping, decolorizing, andcounterstaining. The Gram stain as commonly used in histologylaboratories is known to be inconsistent, in particular, as a result ofvariability in the decolorizing step. Variables affecting thedecolorizing step include solvent strength, concentration, volume, andduration of exposure. During manual Gram staining procedures, thedecolorizing step routinely uses alcohol or acetone, and the step onlytakes a matter of seconds. However, for automated staining procedures,this decolorizing process occurs too quickly. This disclosure addressesthe issues of Gram stain decolorizing on an automated staining platform.

SUMMARY

Provided herein are methods, compositions, and kits that permitautomation of Gram staining. The inventors have identified compositionsthat prolong the decolorizing step of Gram staining, which permitsautomation of Gram staining, for example, using automated and/orcomputer-implemented staining equipment.

Methods are provided for Gram staining a sample, such as a sample on amicroscope slide. Such methods can be used to detect and distinguishGram-positive and Gram-negative bacteria. In some examples, thedisclosed Gram staining methods are used to detect non-bacterialmicroorganisms, such as yeast (e.g., Candida and Cryptococcus).

In particular examples, the methods include contacting the sample with aslow-acting decolorizing formulation (such as one that includes1,2-propanediol or ethylene glycol) under conditions sufficient tosignificantly remove a primary stain-trapping agent complex fromGram-negative bacteria, but not from Gram-positive bacteria. The sampleis one that was previously contacted with a primary stain (such ascrystal violet) and a trapping agent (such as iodine). In particularexamples, the methods include one or more additional steps of the Gramstaining procedure, such as contacting the sample with the primary stainunder conditions sufficient to stain the cell wall and cell membrane ofGram-positive and Gram-negative bacteria; contacting the sample with atrapping agent under conditions sufficient to form a primarystain-trapping agent complex; contacting the sample with a counterstainunder conditions sufficient to stain decolorized Gram-negative bacteria,or combinations thereof.

Also provided are compositions that can act as a slow-actingdecolorizing formulation. In one example, the composition includes atleast 80% of a slow-acting decolorizing agent (such as 1,2-propanediolor ethylene glycol) and no more than 20% of a fast-acting decolorizingagent (such as 0.1 to 20% of a fast-acting decolorizing agent, forexample ethyl alcohol or acetone). Such compositions can be used as theslow-acting decolorizing formulation in an automated Gram stain.

Kits for automated Gram staining are also provided. In one example, thekit includes a slow-acting decolorizing formulation in a container, suchas a formulation that includes at least 80% or at least 90% of aslow-acting decolorizing agent (such as 1,2-propanediol or ethyleneglycol) and no more than 20% of a fast-acting decolorizing agent (suchas 0.1 to 20% or 1 to 10% of a fast-acting decolorizing agent, forexample ethyl alcohol or acetone). In some examples, kits canadditionally include other components, such as one or more of a primarystain in a container, a trapping agent in a container, a counterstain ina container, microscope slides, coverslips, other stains, and controlslides. In particular examples, the container is configured to be usedwith an automated Gram staining platform.

The foregoing and other objects and features of the disclosure willbecome more apparent from the following detailed description, whichproceeds with reference to the accompanying FIGURE.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 is a flow chart showing an exemplary method for automated Gramstaining.

DETAILED DESCRIPTION

The following explanations of terms and methods are provided to betterdescribe the present disclosure and to guide those of ordinary skill inthe art in the practice of the present disclosure. The singular forms“a,” “an,” and “the” refer to one or more than one, unless the contextclearly dictates otherwise. For example, the term “comprising aspecimen” includes single or plural specimens and is consideredequivalent to the phrase “comprising at least one specimen.” The term“or” refers to a single element of stated alternative elements or acombination of two or more elements, unless the context clearlyindicates otherwise. As used herein, “comprises” means “includes.” Thus,“comprising A or B,” means “including A, B, or A and B,” withoutexcluding additional elements.

Unless explained otherwise, all technical and scientific terms usedherein have the same meaning as commonly understood to one of ordinaryskill in the art to which this disclosure belongs. In case of conflict,the present specification, including explanations of terms, willcontrol. Explanation of common terms and methods in microbiology may befound in Wistreich and Lechtman, Laboratory Exercises in Microbiology,6^(th) Edition, 1988 and Boyd, General Microbiology, 2^(nd) Edition,1988.

All publications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety for allpurposes.

Although methods and materials similar or equivalent to those describedherein can be used to practice or test the disclosed technology,suitable methods and materials are described below. The materials,methods, and examples are illustrative only and not intended to belimiting.

To facilitate review of the various embodiments of this disclosure, thefollowing explanations of specific terms are provided:

Antibody (Ab): A polypeptide that includes at least a light chain orheavy chain immunoglobulin variable region and specifically binds anepitope of an antigen (such as a target agent). Antibodies includemonoclonal antibodies, polyclonal antibodies, or fragments of antibodiesas well as others known in the art. In some examples, an antibody isspecific for a target, such as a particular bacterium or type ofbacterium, and thus can be used in a companion assay with the Gramstaining methods provided herein.

Antibodies are composed of a heavy and a light chain, each of which hasa variable region, termed the variable heavy (VH) region and thevariable light (VL) region. Together, the VH region and the VL regionare responsible for binding the antigen recognized by the antibody. Thisincludes intact immunoglobulins and the variants and portions of themwell known in the art, such as Fab′ fragments, F(ab)′2 fragments, singlechain Fv proteins (“scFv”), and disulfide stabilized Fv proteins(“dsFv”). A scFv protein is a fusion protein in which a light chainvariable region of an immunoglobulin and a heavy chain variable regionof an immunoglobulin are bound by a linker, while in dsFvs, the chainshave been mutated to introduce a disulfide bond to stabilize theassociation of the chains. The term also includes recombinant forms suchas chimeric antibodies (for example, humanized murine antibodies) andheteroconjugate antibodies (such as, bispecific antibodies). See also,Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford,Ill.); Kuby, Immunology, 3rd Ed., W.H. Freeman & Co., New York, 1997.

A “monoclonal antibody” is an antibody produced by a single clone of Blymphocytes or by a cell into which the light and heavy chain genes of asingle antibody have been transfected. Monoclonal antibodies areproduced by methods known to those of ordinary skill in the art, forinstance by making hybrid antibody-forming cells from a fusion ofmyeloma cells with immune spleen cells. These fused cells and theirprogeny are termed “hybridomas.” Monoclonal antibodies include humanizedmonoclonal antibodies.

Bacteria: Prokaryotic organisms that in some examples cause disease(pathogenic bacteria). Bacteria can be classified based on thestructural characteristics of their cell walls. For example, the thicklayers of peptidoglycan in the “Gram-positive” cell wall stain purple,while the thin “Gram-negative” cell wall appears pink. By combiningmorphology and Gram-staining, most bacteria can be classified asbelonging to one of four groups (Gram-positive cocci, Gram-positivebacilli, Gram-negative cocci and Gram-negative bacilli).

Examples of bacteria that can be detected with the disclosed Gramstaining methods, include without limitation: Acinetobacter baumanii,Actinobacillus sp., Actinomycetes, Actinomyces sp. (such as Actinomycesisraelii and Actinomyces naeslundii), Aeromonas sp. (such as Aeromonashydrophila, Aeromonas veronii biovar sobria (Aeromonas sobria), andAeromonas caviae), Anaplasma phagocytophilum, Alcaligenes xylosoxidans,Acinetobacter baumanii, Actinobacillus actinomycetemcomitans, Bacillussp. (such as Bacillus anthracis, Bacillus cereus, Bacillus subtilis,Bacillus thuringiensis, and Bacillus stearothermophilus), Bacteroidessp. (such as Bacteroides fragilis), Bartonella sp. (such as Bartonellabacilliformis and Bartonella henselae, Bifidobacterium sp., Bordetellasp. (such as Bordetella pertussis, Bordetella parapertussis, andBordetella bronchiseptica), Borrelia sp. (such as Borrelia recurrentis,and Borrelia burgdorferi), Brucella sp. (such as Brucella abortus,Brucella canis, Brucella melintensis and Brucella suis), Burkholderiasp. (such as Burkholderia pseudomallei and Burkholderia cepacia),Campylobacter sp. (such as Campylobacter jejuni, Campylobacter coli,Campylobacter lari and Campylobacter fetus), Capnocytophaga sp.,Cardiobacterium hominis, Chlamydia trachomatis, Chlamydophilapneumoniae, Chlamydophila psittaci, Citrobacter sp. Coxiella burnetii,Corynebacterium sp. (such as, Corynebacterium diphtheriae,Corynebacterium jeikeum and Corynebacterium), Clostridium sp. (such asClostridium perfringens, Clostridium difficile, Clostridium botulinumand Clostridium tetani), Eikenella corrodens, Enterobacter sp. (such asEnterobacter aerogenes, Enterobacter agglomerans, Enterobacter cloacaeand Escherichia coli, including opportunistic Escherichia coli, such asenterotoxigenic E. coli, enteroinvasive E. coli, enteropathogenic E.coli, enterohemorrhagic E. coli, enteroaggregative E. coli anduropathogenic E. coli) Enterococcus sp. (such as Enterococcus faecalisand Enterococcus faecium) Ehrlichia sp. (such as Ehrlichia chafeensiaand Ehrlichia canis), Erysipelothrix rhusiopathiae, Eubacterium sp.,Francisella tularensis, Fusobacterium nucleatum, Gardnerella vaginalis,Gemella morbillorum, Haemophilus sp. (such as Haemophilus influenzae,Haemophilus ducreyi, Haemophilus aegyptius, Haemophilus parainfluenzae,Haemophilus haemolyticus and Haemophilus parahaemolyticus, Helicobactersp. (such as Helicobacter pylori, Helicobacter cinaedi and Helicobacterfennelliae), Kingella kingii, Klebsiella sp. (such as Klebsiellapneumoniae, Klebsiella granulomatis and Klebsiella oxytoca),Lactobacillus sp., Listeria monocytogenes, Leptospira interrogans,Legionella pneumophila, Leptospira interrogans, Peptostreptococcus sp.,Moraxella catarrhalis, Morganella sp., Mobiluncus sp., Micrococcus sp.,Mycobacterium sp. (such as Mycobacterium leprae, Mycobacteriumtuberculosis, Mycobacterium intracellulare, Mycobacterium avium,Mycobacterium Bovis, and Mycobacterium marinum), Mycoplasm sp. (such asMycoplasma pneumoniae, Mycoplasma hominis, and Mycoplasma genitalium),Nocardia sp. (such as Nocardia asteroides, Nocardia cyriacigeorgica andNocardia brasiliensis), Neisseria sp. (such as Neisseria gonorrhoeae andNeisseria meningitidis), Pasteurella multocida, Plesiomonasshigelloides. Prevotella sp., Porphyromonas sp., Prevotellamelaninogenica, Proteus sp. (such as Proteus vulgaris and Proteusmirabilis), Providencia sp. (such as Providencia alcalifaciens,Providencia rettgeri and Providencia stuartii), Pseudomonas aeruginosa,Propionibacterium acnes, Rhodococcus equi, Rickettsia sp. (such asRickettsia rickettsii, Rickettsia akari and Rickettsia prowazekii,Orientia tsutsugamushi (formerly: Rickettsia tsutsugamushi) andRickettsia typhi), Rhodococcus sp., Serratia marcescens,Stenotrophomonas maltophilia, Salmonella sp. (such as Salmonellaenterica, Salmonella typhi, Salmonella paratyphi, Salmonellaenteritidis, Salmonella cholerasuis and Salmonella typhimurium),Serratia sp. (such as Serratia marcesans and Serratia liquifaciens),Shigella sp. (such as Shigella dysenteriae, Shigella flexneri, Shigellaboydii and Shigella sonnei), Staphylococcus sp. (such as Staphylococcusaureus, Staphylococcus epidermidis, Staphylococcus hemolyticus,Staphylococcus saprophyticus), Streptococcus sp. (such as Streptococcuspneumoniae (for example chloramphenicol-resistant serotype 4Streptococcus pneumoniae, spectinomycin-resistant serotype 6BStreptococcus pneumoniae, streptomycin-resistant serotype 9VStreptococcus pneumoniae, erythromycin-resistant serotype 14Streptococcus pneumoniae, optochin-resistant serotype 14 Streptococcuspneumoniae, rifampicin-resistant serotype 18C Streptococcus pneumoniae,tetracycline-resistant serotype 19F Streptococcus pneumoniae,penicillin-resistant serotype 19F Streptococcus pneumoniae, andtrimethoprim-resistant serotype 23F Streptococcus pneumoniae,chloramphenicol-resistant serotype 4 Streptococcus pneumoniae,spectinomycin-resistant serotype 6B Streptococcus pneumoniae,streptomycin-resistant serotype 9V Streptococcus pneumoniae,optochin-resistant serotype 14 Streptococcus pneumoniae,rifampicin-resistant serotype 18C Streptococcus pneumoniae,penicillin-resistant serotype 19F Streptococcus pneumoniae, ortrimethoprim-resistant serotype 23F Streptococcus pneumoniae),Streptococcus agalactiae, Streptococcus mutans, Streptococcus pyogenes,Group A streptococci, Streptococcus pyogenes, Group B streptococci,Streptococcus agalactiae, Group C streptococci, Streptococcus anginosus,Streptococcus equismilis, Group D streptococci, Streptococcus Bovis,Group F streptococci, and Streptococcus anginosus Group G streptococci),Spirillum minus, Streptobacillus moniliformi, Treponema sp. (such asTreponema carateum, Treponema petenue, Treponema pallidum and Treponemaendemicum, Tropheryma whippelii, Ureaplasma urealyticum, Veillonellasp., Vibrio sp. (such as Vibrio cholerae, Vibrio parahemolyticus, Vibriovulnificus, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrioalginolyticus, Vibrio mimicus, Vibrio hollisae, Vibrio fluvialis, Vibriometchnikovii, Vibrio damsela and Vibrio furnisii), Yersinia sp. (such asYersinia enterocolitica, Yersinia pestis, and Yersiniapseudotuberculosis) and Xanthomonas maltophilia among others.

Contact: Placement in direct physical association; includes both insolid and liquid form. For example, contacting can occur in vitrobetween a reagent (such as a component of a Gram stain) and a samplethat is either in solution or on a surface (for example on a microscopeslide).

Decolorizing agent: An agent that can substantially remove a primarystain (e.g., crystal violet) and trapping agent (e.g., iodine) complexfrom a sample (e.g., a sample stained with a primary stain and trappingagent), such as substantial removal of the complex from the cell wall ofGram-negative bacteria, but not Gram-positive bacteria. In one example,such a complex is referred to as a crystal violet-iodine (CV-I) complex.In particular examples, the decolorizing agent is incubated with thesample containing primary stain-trapping agent complexes (e.g., CV-Icomplexes) for a period of time sufficient to substantially remove thecomplexes (and thus the primary stain) from the Gram-negative cells(such as at least 90%, at least 95%, or at least 99% complex removal),but not substantially from Gram-positive cells.

Decolorizing formulation: A composition that includes one or moredecolorizing agents. A slow-acting decolorizing formation or agent isone that requires longer amounts of time to remove primarystain-trapping agent (e.g., CV-I) complexes (and thus the primary stain,e.g., crystal violet) from the Gram-negative cells, for example anamount of time that permits automated equipment to complete thedecolorizing step, thus maintaining the ability of the automatedequipment to control completion of the decolorizing step before moredecolorizing occurs than is desirable (such as decolorizingGram-positive bacteria). In some examples, a slow-acting decolorizingformation takes at least 30 seconds, at least 60 seconds, at least 120seconds, or at least 220 seconds, for example 1 to 4 minutes to removeprimary stain-trapping agent (e.g., CV-I) complexes from Gram negativebacteria. Examples include 1,2-propanediol and ethylene glycol. Afast-acting decolorizing agent is one that requires only a short amountof time to remove primary stain-trapping agent (e.g., CV-I) complexes(and thus the primary stain, e.g., crystal violet) from theGram-negative cells, such as less than 20 seconds, less than 15 seconds,less than 10 seconds, or less than 5 seconds, for example 1 to 2seconds, 1 to 5 seconds, 1 to 10 seconds or 1 to 20 seconds. Examplesinclude ethyl alcohol, acetone, diethyl ether, methyl ether, blends ofethyl alcohol and acetone, and blends of ethyl alcohol with otheralcohols such as methanol or 2-propanol.

Detect: To determine if an agent (such as a signal or particularorganism, such as a Gram-positive or Gram-negative bacterium) is presentor absent, for example a particular bacterium. In some examples, thiscan further include quantification. For example, use of the disclosedmethods and reagents in particular examples permits reporting ofstronger and weaker signals.

Gram-positive bacteria: Bacteria that stain dark blue or violet duringGram staining, and have a thick peptidoglycan layer. ExemplaryGram-positive bacteria include:

Actinobacteria Actinomyces Actinomyces israelii Bacillales BacillusClostridium Clostridium acetobutylicum Clostridium aerotoleransClostridium argentinense Clostridium baratii Clostridium beijerinckiiClostridium bifermentans Clostridium botulinum Clostridium butyricumClostridium cadaveris Clostridium cellulolyticum Clostridium chauvoeiClostridium clostridioforme Clostridium colicanis Clostridium difficileClostridium estertheticum Clostridium fallax Clostridium formicaceticumClostridium histolyticum Clostridium innocuum Clostridium kluyveriClostridium ljungdahlii Clostridium novyi Clostridium paraputrificumClostridium perfringens Clostridium phytofermentans Clostridiumpiliforme Clostridium ragsdalei Clostridium ramosum Clostridium septicumClostridium sordellii Clostridium sporogenes Clostridium sticklandiiClostridium tertium Clostridium tetani Clostridium thermosaccharolyticumClostridium tyrobutyricum Corynebacterium Corynebacterium bovisCorynebacterium diphtheriae Corynebacterium granulosum Corynebacteriumjeikeium Corynebacterium minutissimum Corynebacterium renaleEnterococcus Lactobacillales Listeria Nocardia Nocardia asteroidesNocardia brasiliensis Propionibacterium acnes Rhodococcus equi SarcinaSolobacterium moorei Staphylococcus Staphylococcus aureus Staphylococcuscapitis Staphylococcus caprae Staphylococcus epidermidis Staphylococcushaemolyticus Staphylococcus hominis Staphylococcus lugdunensisStaphylococcus muscae Staphylococcus nepalensis Staphylococcuspettenkoferi Staphylococcus saprophyticus Staphylococcus succinusStaphylococcus warneri Staphylococcus xylosus Strangles StreptococcusStreptococcus agalactiae Streptococcus anginosus Streptococcus bovisStreptococcus canis Streptococcus iniae Streptococcus lactariusStreptococcus mitis Streptococcus mutans Streptococcus oralisStreptococcus parasanguinis Streptococcus peroris Streptococcuspneumoniae Streptococcus pyogenes Streptococcus ratti Streptococcussalivarius Streptococcus sanguinis Streptococcus sobrinus Streptococcussuis Streptococcus salivarius thermophilus Streptococcus uberisStreptococcus vestibularis Streptococcus viridans

Gram-negative bacteria: Bacteria that loose or do not retain dark blueor violet stain during Gram staining, but instead are colored by acounterstain, such as safranin, and appear pink or ed. Gram-negativebacteria have a thin peptidoglycan layer. Exemplary Gram-negativebacteria include:

Acetic acid bacteria Fusobacterium necrophorum Acinetobacter baumanniiFusobacterium nucleatum Agrobacterium tumefaciens Fusobacteriumpolymorphum Anaerobiospirillum Haemophilus haemolyticus BacteroidesHaemophilus influenzae Bacteroides fragilis Helicobacter BdellovibrioHelicobacter pylori Brachyspira Klebsiella pneumoniae Cardiobacteriumhominis Legionella Coxiella burnetii Legionella pneumophilaCyanobacteria Leptotrichia buccalis Cytophaga Megamonas DialisterMegasphaera Enterobacter Moraxella Enterobacter cloacae Moraxella bovisEnterobacteriaceae Moraxella catarrhalis Escherichia Moraxella osloensisEscherichia coli Morganella morganii Pseudomonas genome databaseNegativicutes Rickettsia rickettsii Neisseria gonorrhoeae SalmonellaNeisseria meningitidis Salmonella enterica Neisseria sicca Salmonellaenterica enterica Pectinatus Selenomonadales Propionispora Serratiamarcescens Proteobacteria Shigella Proteus mirabilis Spirochaeta Proteuspenneri Spirochaetaceae Pseudomonas Sporomusa Pseudomonas aeruginosaStenotrophomonas Streptococcus gordonii Vampirococcus VerminephrobacterVibrio cholerae Wolbachia Zymophilus

Primary stain: In Gram staining, it is the first dye applied to asample. An example of a primary stain is crystal violet dye.

Quantitating: Determining or measuring a quantity (such as a relativequantity) of a target, such as the quantity of a target bacteriumpresent in a sample.

Reference value: A number or range of numbers representing a particularcondition. An experimental value can be compared to the reference value,for example to make a diagnosis or prognosis. For example, a referencevalue can be a relative or absolute, maximum or minimum amount (orrange) of color expected to define a positive or negative result, suchas Gram-positive or Gram-negative.

Slide: Traditionally a substrate used to mount or attach a sample to formicroscopy, which is typically but not necessarily transparent to light.Samples may be processed before and/or after mounting onto a slide. Insome examples, a slide may be more or less transparent or opaque andmade of glass, silica, quartz, or any other material amenable toGram-staining. A slide may be configured to accommodate one or morespecimens from one or more subjects. A slide as used herein alsoincludes non-traditional substrates such as a tape, a disc, a plate, orany other flat, curved, rectangular, or round surface or shape amenableto presenting a sample for Gram-staining.

Subject: Living or deceased multi-cellular organisms, a category thatincludes plants as well as human and non-human animals, such asveterinary subjects (e.g., birds, cats, dogs, cows, pigs, horses, androdents). In one example, a subject is known or suspected of having abacterial infection.

Trapping agent: An agent that forms a complex with a dye and thenreduces or slows the extent to which the dye may be rinsed from thesample or substrate. In a Gram stain protocol, Iodine is an exampletrapping agent. The trapping agent is sometimes referred to as a mordantbut is more accurately a trapping agent. A mordant binds more tightly tothe substrate and is not easily rinsed out, and in Gram staining, somecapacity to be removed through rinsing is required to avoid falsepositives. A mordant forms a complex with a dye that then additionallybinds a substrate, such as a fabric, and then strongly prevents removalof the dye through rinsing. A trapping agent also forms a complex with adye, but that complex only impedes removal of the dye during rinsing.The mechanism of trapping action is often unknown, but may be due tobeneficial retarding of diffusion or steric hindrances. Trapping agentslikely do not act through strong bonding with a substrate, and typicallya dye in complex with a trapping agent may still be removed under theright conditions, such as through sufficiently long application of asufficiently strong decolorizing agent, as in Gram staining.

Under conditions sufficient for: A phrase that is used to describe anyenvironment that permits the desired activity. This includes bringing areagent into contact with a sample under conditions that allow thereagent to physically or chemically interact or react with, diffusethrough, or displace other components of the sample. In a specificexample, this includes contacting a sample (such as one know orsuspected of containing a bacterium) with one or more reagents orcomponents of the Gram stain, to permit accurate detection ofGram-negative or Gram-positive bacteria in the sample.

Overview

The Gram stain is a well known, commonly used microbiological techniquefor the detection, classification, and identification of microorganisms,especially bacteria, such as the differentiation of bacteria into twogeneral classes based on their cell membrane structures: Gram-positiveand Gram-negative. The principal difference between Gram-positive andGram-negative bacteria is that in Gram-positive bacteria, the primarystaining reagents are absorbed within the whole cellular structure,while in the Gram-negative bacteria, staining occurs only superficially.Consequently, when the sample is subsequently treated with adecolorizing agent, Gram-negative bacteria tend to lose their color,while Gram-positive bacteria normally remain stained blue or violet.

The Gram stain is prone to inconsistent and variable results. Inparticular, the decolorizing step can be problematic with respect toachieving the proper amount of decolorization of the bacteria. If thereis not enough decolorizing, Gram-negative bacteria retain the primarystain (e.g., crystal violet), while if there is too much decolorizing,both Gram-positive and Gram-negative bacteria are destained. Theinconsistencies in decolorizing can be attributed to the affinity of theprimary stain-trapping agent complex for the decolorizing solvent, theamount of decolorizing solvent applied, the relative solubilizingstrength of the decolorizing solvent, as well as the amount of time thedecolorizing solvent is in contact with the sample.

In traditional manual Gram staining methods the decolorizing steprequires only a small volume (such as 2-3 drops) and takes only a fewseconds to decolorize the Gram-negative bacteria. Gram stains areconventionally prepared and analyzed manually. However, this is too fastfor automated procedures, which due to limitations of theinstrumentation, can require minutes at this step. As a result, whentraditional decolorizing agents are used in an automated system, anunacceptable amount of decolorizing occurs. Thus, provided herein arenew slower-acting decolorizing agents and formulations that prolong thedecolorizing step and permit Gram staining to be automated.

Methods of Gram Staining

Gram staining traditionally includes four steps, each of which appliesto the sample one of the following reagents: a primary stain, commonlycrystal violet dye; a trapping agent (sometimes referred to as amordant), commonly iodine; a decolorizing agent, commonly ethanol orethanol/acetone; and a counterstain, usually containing safranin O,fuchsin, or other red dye. The present disclosure provides methods ofimproving on the prior manual methods of Gram staining that included avery rapid decolorizing step (e.g., 1-5 seconds). The disclosed methodsfor Gram staining can be used in automated process, as slow-actingdecolorizing agents been identified that prolong the decolorizing step(e.g., decolorizing takes at least 30 seconds or at least 60 seconds).

The disclosure provides methods of Gram staining a sample. Such methodscan be used to detect and distinguish Gram-positive and Gram-negativebacteria present in the sample. In particular examples, the methodincludes contacting a sample (or a plurality of samples) with aslow-acting decolorizing formulation under conditions sufficient toremove a primary stain-trapping agent complex (e.g., CV-I complex) fromGram-negative bacteria but not Gram-positive bacteria, wherein thesample was previously contacted with a primary stain and a trappingagent.

It will be appreciated that in some examples, the method furtherincludes one or more other steps of Gram staining. For example, themethod can further include one or more of: contacting the sample with aprimary stain under conditions sufficient to stain the cell wall (whichincludes peptidoglycan) (and in some examples the cell membrane) ofGram-positive and Gram-negative bacteria, contacting the sample with atrapping agent under conditions sufficient to form a primarystain-trapping agent complex, which can prevent removal of the primarystain from the Gram-positive bacteria but not Gram-negative bacteria,and contacting the sample with a counterstain under conditionssufficient to stain the cell wall (which includes peptidoglycan) (and insome examples the cell membrane) of decolorized Gram-negative bacteria.

Contacting the sample with a primary stain can include contacting orincubating the sample with a formulation that includes crystal violet(CV) or Gentian violet. In one example, the primary stain formulationincludes CV or Gentian violet at a concentration of at least 0.5 g/L, atleast 0.75 g/L, at least 1 g/L, at least 2 g/L, at least 3 g/L, at least4 g/L, or at least 5 g/L, such as 1 to 4 g/L, for example 3 g/L. In someexamples, the CV or Gentian violet is present in a solution containingisopropanol, ethanol/methanol, and water, such as 50 ml isopropanol, 50ml ethanol/methanol, and 900 ml water. In some examples, the CV orGentian violet solution contains ammonium oxalate to enhance stability.

Contacting the sample with a trapping agent can include contacting orincubating the sample with a formulation that includes iodine, such asGram iodine or polyvinylpyrrolidone-iodine (PVP-iodine) solution. Gramiodine is a mixture that can include at least 0.1% iodine (e.g., atleast 0.2%, at least 0.5%, or at least 1%, such as about 0.1%-1% iodine)and at least 0.1% potassium iodine (e.g., at least 0.2%, at least 0.5%,at least 1%, at least 1.5%, or at least 2%, such as about 0.1%-2%potassium iodine), for example in water or alcohol mixtures. PVP-iodineincludes at least 1% polyvinylpyrrolidone (e.g., at least 2%, at least5%, at least 10%, at least 20%, at least 30%, or at least 35%, such asabout 1-35% polyvinylpyrrolidone) and at least 1% iodine (e.g., at least2%, at least 5%, at least 10%, at least 20%, at least 30%, or at least35%, such as about 1%-35% iodine) in water (e.g., see U.S. Pat. Nos.2,739,922 and 3,898,326).

Contacting the sample with a counterstain can include contacting orincubating the sample with a formulation that includes fuchsin (such asbasic fuchsin or carbol fuchsin), neutral red, and/or safranin 0. In oneexample, the counterstain formulation includes fuchsin at aconcentration of at least 0.01%, at least 0.02%, at least 0.03%, atleast 0.05%, at least 0.1%, at least 0.2%, at least 0.3%, at least 0.4%,or at least 0.5%, such as from 0.02% to 0.5%. In one example, thecounterstain formulation includes neutral red at a concentration of atleast 0.01%, at least 0.02%, at least 0.03%, at least 0.05%, at least0.1%, at least 0.2%, at least 0.3%, at least 0.4%, or at least 0.5%,such as from 0.02% to 1%. In one example, the counterstain formulationincludes safranin 0 at concentration of at least at 0.1%, such as atleast at 0.2%, at least at 0.3%, at least at 0.4%, at least at 0.5%, atleast at 0.6%, at least at 0.7%, or at least at 0.8%, such as 0.1% to 1%or 0.1% to 0.8% safranin 0. The counterstain can be formulated in water,but in some examples may include 1%-20% ethanol or methanol.

In some examples, the sample is incubated with the slow-actingdecolorizing formulation and the counterstain at the same time. In someexamples, the concentration of slow-acting decolorizing formulation in acombined slow-acting decolorizing formulation/counterstainingformulation can range from about 75% to 99%, such as at least 75%slow-acting decolorizing formulation, at least 80% slow-actingdecolorizing formulation, at least 90% slow-acting decolorizingformulation, or at least 95% slow-acting decolorizing formulation. Inother examples, the sample is first incubated with the slow-actingdecolorizing formulation followed by the counterstain.

One skilled in the art will appreciate that each contacting step of theGram stain method can include or be followed by a rinsing step, prior tothe next contacting step. Rinsing can be accomplished using anysubsequent formulation capable of washing away a previous formulationwithout an undesirable reaction. For example, the subsequent formulationmay be one of the next Gram stain formulations, brought into contactwith the sample in excess quantity and allowed to drain away, in whichcase rinsing is effectively combined with contacting a sample with thenext Gram stain formulation (e.g., in the order shown in FIG. 1). Inanother example, separate rinsing steps are added after or as part ofthe contacting steps (e.g., those shown in FIG. 1). In this example,rinsing occurs when a sample is contacted with an inactive formulation(e.g., water or buffer), and then allowed to drain away.

In some examples, the amount of time the sample is contacted with orincubated with the slow-acting decolorizing formulation is longer thantraditional manual Gram staining. For example, use of a slow-actingdecolorizing formulation requires longer amounts of time to removeprimary stain-trapping agent (e.g., CV-I) complexes (and thus theprimary stain, e.g., crystal violet) from the Gram-negative cells. Insome examples, the sample is contacted with or incubated with theslow-acting decolorizing formulation at least 30 seconds, at least 45seconds, at least 60 seconds, at least 120 seconds, or at least 220seconds, for example 30 seconds to 4 minutes, 1 to 5 minutes, or 2 to 4minutes. In some examples, longer periods of decolorizing permitautomated equipment to complete the decolorizing step, thus maintainingthe ability of the automated equipment to control completion of thedecolorizing step before more decolorizing occurs than is desirable(such as decolorizing Gram-positive bacteria). Thus, in some examples,the time between or at one or more steps is designed to conform toautomation, such as automation of the Gram stain by a particular pieceof equipment.

In one example, the sample is incubated or contacting with the primarystain, trapping agent, or counterstain for at least 30 seconds, at least40 seconds, at least 50 seconds, at least 60 seconds, at least 70seconds, at least 80 seconds, at least 90 seconds, at least 100 seconds,at least 120 seconds, at least 150 seconds, at least 180 seconds, atleast 210 seconds, at least 220 seconds, at least 240 seconds, at least270 seconds, or at least 300 seconds. In addition, after contacting asample with any or each of the Gram stain formulations (primary stain,trapping agent, slow-acting decolorizing formulation and counterstain),subsequent contacting of the sample with a rinse formulation or with anysubsequent Gram stain formulation can in some example occur after atleast approximately 10 seconds, 20 seconds, 30 seconds, 40 seconds, 50seconds, 60 seconds, 70 seconds, 80 seconds, 90 seconds, 100 seconds,120 seconds, 150 seconds, 180 seconds, 210 seconds, 240 seconds, 270seconds, or 300 seconds have elapsed. Thus for example, after contactingthe sample with a primary stain, contacting with the trapping agent canoccur at least 10 seconds later, such as at least 30 seconds, or atleast 1 minute later. In examples in which separate rinse steps usinginactive formulations are included, subsequent to that rinse step,contacting with the next Gram stain formulation can occur after at leastapproximately 0.5 seconds, 1 second, 2 seconds, 4 seconds, 6 seconds, 8seconds, 10 seconds, 20 seconds, 30 seconds, 40 seconds, 50 seconds, 60seconds, 70 seconds, 80 seconds, 90 seconds, 100 seconds, 120 seconds,150 seconds, 180 seconds, 210 seconds, 240 seconds, 270 seconds, or 300seconds have elapsed.

The temperature of the reagents used in the Gram staining methods can beambient or be controlled by automated equipment and local facilities tobe the same for each formulation or to vary for one or moreformulations. In one example, inactive rinse formulations are relativelycolder than ambient air temperature. In some examples, inactive rinseformulations are in the range of 5° to 50° C. immediately prior to beingbrought into contact with a sample. In some examples, one or more of theGram stain formulations (primary stain, trapping agent, slow-actingdecolorizing formulation and counterstain) are at 10° to 60° C.immediately prior to being brought into contact with a sample.

In some examples, the pH of a Gram stain formulation is adjusted, andcan include acids, bases, and buffering agents. In some examples, one ormore of the Gram stain formulations (primary stain, trapping agent,slow-acting decolorizing formulation and counterstain) are at pH=3 topH=8, for example to achieve better staining and for distinguishingbacterial cells from non-bacterial cells following Gram staining.

In some examples, the method further includes detecting theGram-positive or Gram-negative bacteria in the sample, for example witha microscope or other similar equipment. For example, the method caninclude determining whether the analyzed sample contains Gram-positiveand/or Gram-negative bacteria.

The disclosed methods are exemplified in FIG. 1, which shows anexemplary automated staining method, 100, which includes a Gram stainingprocedure 101. The Gram stain procedure 101 shown in FIG. 1 has stepsthat include: contacting the sample with a primary stain formulation107, contacting the sample with trapping formulation 108, contacting thesample with a slow-acting decolorizing formulation 109, contacting asample with a counterstain formulation 110, and classifying the sample111 as Gram-positive, Gram-negative, or indeterminate. Thus, the methodincludes contacting the sample with the slow-acting decolorizingformulation, 109. FIG. 1 shows that contacting the sample with theslow-acting decolorizing formulation 109 occurs after the sample hasbeen contacted with the primary stain formulation 107 and by thetrapping formulation 108, but before contacting the sample with thecounterstain formulation 110. As discussed above, each contacting step107, 108, 109, and 110, can include or be followed by additional rinsingsteps, prior to the next contacting step. For example, after the sampleis contacted with the primary stain formulation 107, it can be rinsedprior to or during contacting the sample with the trapping formulation108. The method can also include step 111 of classifying or determiningwhether the bacteria in the sample are Gram-negative, Gram-positive, orwhether it is not possible to make such a determination.

Thus, after contacting a sample with any or each of the Gram stainformulations of FIG. 1 (107, 108, 109, and/or 110), the subsequentcontacting with a rinse formulation or with the subsequent Gram stainformulation can occur after at least approximately 10 seconds, 20seconds, 30 seconds, 40 seconds, 50 seconds, 60 seconds, 70 seconds, 80seconds, 90 seconds, 100 seconds, 120 seconds, 150 seconds, 180 seconds,210 seconds, 215 seconds, 220 seconds, 240 seconds, 270 seconds, or 300seconds have elapsed. In examples in which separate rinse steps usinginactive formulations are included, subsequent to that rinse step,contacting with the next Gram stain formulation of FIG. 1 (107, 108,109, and/or 110) may occur after at least approximately 0.5 seconds, 1second, 2 seconds, 4 seconds, 6 seconds, 8 seconds, 10 seconds, 20seconds, 30 seconds, 40 seconds, 50 seconds, 60 seconds, 70 seconds, 80seconds, 90 seconds, 100 seconds, 120 seconds, 150 seconds, 180 seconds,210 seconds, 240 seconds, 270 seconds, or 300 seconds have elapsed.

As shown in FIG. 1, in a method for automated Gram staining 100, themethod can include steps for obtaining a sample 102 and loading thesample 103 into the automated equipment. The automated equipment mayperform assays in parallel 105 or in series preceding 104, or following106, Gram staining steps 101. Preceding 104 and following series assays106 can be performed on the same sample, but for example differentslides. Examples of preceding 104 and following series assays 106include immunoassays and additional microbiological assays.

Automation

In some examples, one or more of the Gram staining steps (e.g.,contacting a sample with a primary stain formulation, trapping agentformulation, slow-acting decolorizing agent formulation, and/orcounterstain formulation) occur using automatic staining equipment. Forexample, the disclosed methods can be used with Ventana Medical Systems,Inc. equipment such as the Ventana NexES Special Stainer, VentanaBenchMark Special Stainer, Benchmark XT, Benchmark Ultra, and Discoverysystems. Exemplary systems are disclosed in U.S. Pat. No. 6,352,861,U.S. Pat. No. 5,654,200, U.S. Pat. No. 6,582,962, U.S. Pat. No.6,296,809, and U.S. Pat. No. 5,595,707, and additional informationconcerning automated systems and methods also can be found inPCT/US2009/067042.

In some examples, the method for automated Gram staining is acomputer-implemented method in which an algorithm, a computer within theautomated equipment, a separate computer, and/or a distributed computersystem and/or network contribute to execution of any or all of the Gramstaining steps (e.g., one or more of the steps in FIG. 1, such as steps107, 108, 109, 110, and 111 of FIG. 1) via computer-executableinstructions in one or more computer-readable media. For example,computer implementation of the disclosed Gram staining method (e.g., asshown in FIG. 1) may contribute to tracking of samples, selection and/ortiming of assays and/or steps of assays, control of equipment,acquisition and/or analysis of results, data retention, reporting to andinterface with medical or other information systems, decision making,changes to sample flow, and/or notifications to operators and otherpersonnel.

In automated Gram staining methods, automated equipment may require moretime to process multiple samples and proceed than traditional manualGram staining methods, such as minutes rather than seconds. For example,the decolorizing step can be adjusted in terms of duration, as well asvolume and solvating strength, to adequately remove primarystain-trapping agent complex (e.g., CV-I complex) from only theGram-negative bacteria. However, for automated systems, like the VentanaMedical Systems, Inc. NexES Special Stainer, BenchMark Special Stainer,Benchmark XT, Benchmark Ultra, or Discovery systems, in which the timebetween dispense/application and rinsing/removal is fixed to definiteminimum value, control of the decolorizing step is constrained tochanging either the volume or solvating strength of the decolorizingformulation. If the volume is too small, inconsistent decolorizing canoccur, and it may not be possible to alter the solvating strength ofethanol to allow for selective decolorizing of the primarystain-trapping agent complex (e.g., CV-I complex) from only theGram-negative bacteria. For example, the Ventana BenchMark SpecialStainer operates within a defined, invariable lockstep between the twoprocesses of dispense and removal, and it is shown herein thatslow-acting decolorizing formulations, such as those that include1,2-propandiol, effectively and selectively decolorizes theGram-negative bacteria within this timeframe.

The automatic staining equipment may operate in part through the use ofcompressed air. Thus, in some examples when the sample is contacted witha primary stain formulation, trapping agent formulation, slow-actingdecolorizing agent formulation, and/or counterstain formulation,compressed air is used to deliver the primary stain formulation,trapping agent formulation, slow-acting decolorizing agent formulation,and/or counterstain formulation, to the sample.

In some examples the method includes loading the sample to be analyzedfor the presence of bacteria into automatic staining equipment.

In a particular example, a method for Gram staining bacteria on a slideusing automatic staining equipment is provided. The automatic stainingequipment can include a carousel means for holding a plurality ofslides, wherein each slide has thereon a sample to be stained, such as asample known or suspected of containing bacteria. The automatic stainingequipment can also include a means for rotating the carousel means atpredetermined speeds and a means for directing and controllingapplication of reagents (such as Gram staining reagents or other stains)onto the slides and samples during rotation of the carousel means. Sucha method can include directing a primary stain reagent (such as onecontaining crystal violet) onto the slides in the carousel to contactthe bacteria on the slides with the primary stain reagent; directingwater, a water-surfactant mixture, or buffer onto the slides in thecarousel to rinse the primary stain reagent from the slides, for exampleunder conditions to permit removal of excess stain; directing a trappingreagent (such as one containing iodine) onto the slides in the carouselto contact the bacteria on the slides with the trapping reagent, forexample under conditions to permit formation of a primary stain-trappingagent complex in the Gram-positive bacteria in the sample, directingwater or other buffer onto the slides in the carousel to rinse excesstrapping reagent from the slides; directing a slow-acting decolorizingformulation and a counterstain, either separately or together, onto theslides in the carousel, for example under conditions to permit removalof primary stain in the Gram-negative bacteria in the sample; anddirecting water or buffer onto the slides in the carousel to rinseexcess slow-acting decolorizing formulation and/or counterstain from theslides (if the slow-acting decolorizing formulation and counterstain areadded separately, the method can include a washing step in between). Themethod can further include detecting the Gram-positive or Gram-negativebacteria on the slide.

Slow-Acting Decolorizing Formulations

The slow-acting decolorizing formulation used in the disclosed methodsrelies on the identification of slow-acting decolorizing agents such as1,2-propanediol and ethylene glycol. It is shown herein that thedecolorizing agent 1,2-propanediol, or propylene glycol (PG) as it iscommonly called, can effectively decolorize the CV-I complex fromGram-negative bacteria within the timed lockstep (4 minutes) of anautomated stainer, for example the BenchMark Special Stainer. PG isslower to dissolve the lyposaccharide layer of Gram-negative bacteriaand allow diffusion of the CV-I complex from the bacterial cell membrane(peptidoglycan) than other decolorizers, thereby allowing selectivedecolorizing of only Gram-negative cells to occur at a slower rate. ThusPG allows a Gram stain to be performed by an automated staining systemhaving a set time between decolorizer application and removal that issubstantially longer than that used with traditional decolorizers.

One or more of these and any other slow-acting decolorizing agents maybe used in pure form, diluted with water or a buffer, or mixed withfast-acting agents in order to create decolorizing formulations ofdesirable rate of decolorizing. In one example, a slow-actingdecolorizing formulation includes a slow-acting decolorizing agent, suchas 1,2-propanediol, ethylene glycol, or combinations thereof. In aspecific example, the slow-acting decolorizing formulation is orconsists of 1,2-propanediol or ethylene glycol. In some examples, watermay be included in the slow-acting decolorizing formulation, for exampleat concentrations ranging from about 0% to 25%, such as 0.5% to 25%, 1%to 20%, 5% to 10%, such as about 10%.

The slow-acting decolorizing formulation can in some examples include amixture of a slow-acting decolorizing agent and a fast-actingdecolorizing agent, such as at least 80%, at least 81%, at least 82%, atleast 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or at least 99.9% of a slow-acting decolorizingagent (e.g., 1,2-propanediol, ethylene glycol, or combinations thereof),such as 80% to 99.99%, 80% to 95%, 90% to 99, or 90% to 95% of aslow-acting decolorizing agent, and no more than 20%, no more than 19%,no more than 18%, no more than 17%, no more than 16%, no more than 15%,no more than 14%, no more than 13%, no more than 12%, no more than 11%,no more than 10%, no more than 9%, no more than 8%, no more than 7%, nomore than 6%, no more than 5%, no more than 4%, no more than 3%, no morethan 2%, no more than 1%, no more than 0.5%, or no more than 0.01% of afast-acting decolorizing agent such as 0.01% to 20%, 1% to 20%, 1% to10%, or 1% to 5% of a fast-acting decolorizing agent. Examples offast-acting decolorizing agents include propyleneglycol methyl ether,diethyl ether, ethanol, acetone, methanol, 1-propanol, 2-propanol,1-butanol, or combinations thereof, such as blends of ethyl alcohol andacetone and blends of ethyl alcohol with other alcohols such as methanolor 2-propanol.

Samples

A sample can be any material to be analyzed for the presence ofbacteria. A sample can be biological or non-biological and can beobtained from a subject, an environment, a system, or a process. Thus,in some examples, the method includes obtaining the sample. For example,the sample can be obtained from a subject known or suspected of having abacterial infection, or from a source known or suspected of beingcontaminated by bacteria.

In one example the sample is obtained from a subject, such as a humansubject. Such a sample can be any solid or fluid sample obtained from,excreted by or secreted by the subject, such as cells, cell lysates,peripheral blood (or a fraction thereof such as serum or plasma), urine,bile, ascites, saliva, cheek swabs, tissue biopsy (such as a tumorbiopsy or lymph node biopsy), surgical specimen, bone marrow,amniocentesis samples, fine needle aspirates, cervical samples (forexample a PAP smear, cells from exocervix, or endocervix), cerebrospinalfluid, aqueous or vitreous humor, a transudate, an exudate (for example,fluid obtained from an abscess or any other site of infection orinflammation), fluid obtained from a joint (for example, a normal jointor a joint affected by disease, such as a rheumatoid arthritis,osteoarthritis, gout or septic arthritis) and autopsy material.

In one example the sample is obtained from the environment, such as froma body of water, air, sediment, dust, soil, or from the interior orsurface of an animate or inanimate object in a natural or a residential,commercial, industrial, medical, academic, agricultural, or otherman-made environment (e.g., food processing, production, and consumptionfacilities and disposal environments), and can be obtained from anindustrial source, such as a farm, waste stream, or water source. Thus,samples can be those obtained from any environment known or suspected toharbor bacteria, microorganisms, or multicellular material generally.

In one example the sample is a food sample (such as a meat, fruit,dairy, or vegetable sample) or a sample obtained from a food-processingplant.

In some examples, the sample is a collected fluid, scraping, filtrand,or culture. In one example, the sample is a cytology sample. Inparticular examples, samples are used directly (e.g., fresh or frozen),or can be manipulated prior to use, for example, by concentration,dilution, fixation (e.g., using formalin or heat) and/or embedding inwax (such as formalin-fixed paraffin-embedded (FFPE) samples). In oneexample, the sample is heat-fixed to a microscope slide.

Additional Assays

In some examples, the disclosed methods can include performingadditional assays on the sample, for example to determine or identifythe particular bacteria in the sample. The additional assays can beperformed before or after the Gram staining, or even simultaneously orcontemporaneously with the Gram staining. Such additional assays areusually performed on a separate slide. For example, a sample can beapplied to a plurality of slides (for example different slices orsections of a FFPE sample), wherein each slide is subjected to aparticular assay. Thus, multiple assays can be performed in paralleland/or in series on the same sample slide, and/or multiple sectionstaken from the same sample and mounted on separate slides, and/or ondifferent samples from the same and/or different subjects mounted on thesame and/or separate slides.

In one example, the sample is subjected to an immunoassay, for exampleby incubation with one or more antibodies specific for a particulartarget bacterium, and detected using a label (such as a label on theantibody or via use of a labeled secondary antibody). Exemplarydetectable labels include fluorophores, haptens, enzymes, radiolabels,quantum dots, and others known in the art.

In another example, the sample is subjected to additionalmicrobiological assays. For example, the sample can be contacted withone or more other dyes, such as one or more of the following stains:Acid Fast Bacilli (AFB) III, Alcian Blue, Alcian Blue for Periodic AcidSchiff (PAS), Alcian Yellow, Congo Red, Diastase, Elastic, Giemsa,Grocott's Methenamine Silver stain (GMS) II, iron, Jones Light Green,Jones, Light Green for PAS, Mucicamine PAS, Reticulum, Steiner II,Trichrome Blue, and Trichrome Green. In one example, the sample iscontacted with Ziehl-Neelsen or similar stains, for example to detectmycobacteria or Nocardia, which show acid-fastness but are sometimedifficult to identify with Gram staining.

Kits

Kits that can be used with the disclosed methods are provided herein. Insome examples, such kits can be used with an automated Gram stainingmethod having a longer decolorizing step (such as a decolorizing stepthat takes at least 30 seconds, at least 1 minute, at least 2 minutes,at least 3 minutes, at least 4 minutes, or at least 5 minutes tocomplete).

In particular examples, the disclosed kits include a slow-actingdecolorizing formulation in a container (e.g., vial or vessel). The kitscan in some examples also include reagents for performing one or more ofthe other steps of the Gram stain method. For example, kits can furtherinclude a primary stain formulation, a trapping agent formulation,and/or a counterstain formulation, for example wherein each formulationis in a separate container.

In one example, the container of the slow-acting decolorizingformulation includes one or more slow-acting decolorizing agents, suchas 1,2-propanediol, ethylene glycol, or combinations thereof. In aspecific example, the slow-acting decolorizing formulation is orconsists of 1,2-propanediol or ethylene glycol. The slow-actingdecolorizing formulation can in some examples include a mixture of aslow-acting decolorizing agent(s) and a fast-acting decolorizingagent(s), such as at least 80%, at least 81%, at least 82%, at least83%, at least 84%, at least 85%, at least 86%, at least 87%, at least88%, at least 89%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or at least 99.9% of one or more slow-actingdecolorizing agents (e.g., 1,2-propanediol, ethyl glycol, orcombinations thereof), such as 80% to 99.99%, 80% to 99%, 80% to 90%,90% to 99.9%, or 90% to 98%, of a slow-acting decolorizing agent, and nomore than 20%, no more than 19%, no more than 18%, no more than 17%, nomore than 16%, no more than 15%, no more than 14%, no more than 13%, nomore than 12%, no more than 11%, no more than 10%, no more than 9%, nomore than 8%, no more than 7%, no more than 6%, no more than 5%, no morethan 4%, no more than 3%, no more than 2%, no more than 1%, no more than0.5%, or no more than 0.01% of one or more fast-acting decolorizingagents (e.g., propyleneglycol methyl ether, diethyl ether, ethanol,acetone, methanol, 1-propanol, 2-propanol, 1-butanol, or combinationsthereof, such as blends of ethyl alcohol and acetone and blends of ethylalcohol with other alcohols such as methanol or 2-propanol), such as0.01% to 20%, 0.1% to 20%, 0.1% to 10%, 1% to 20%, or 1% to 10%, of afast-acting decolorizing agent.

In one example, the container of the primary stain formulation includescrystal violet (CV) or Gentian violet. In one example, the primary stainformulation includes crystal violet at a concentration of at least 0.5g/L, at least 0.75 g/L, at least 1 g/L, at least 2 g/L, at least 3 g/L,at least 4 g/L, or at least 5 g/L, such as 1 to 4 g/L, for example 3/L.In some examples, the CV is present in a solution containingisopropanol, ethanol/methanol, and water, such as 50 ml isopropanol, 50ml ethanol/methanol, and 900 ml water. In some examples, the CV orGentian violet solution contains ammonium oxalate to enhance stability.

In one example, the container of the trapping agent formulation includesiodine, such as Gram iodine or polyvinylpyrrolidone-iodine (PVP-iodine)solution. Gram iodine can in some examples include at least 0.1% iodine(e.g., at least 0.2%, at least 0.5%, or at least 1%, such as about0.1%-1% iodine) and at least 0.1% potassium iodine (e.g., at least 0.2%,at least 0.5%, at least 1%, at least 1.5%, or at least 2%, such as about0.1%-2% potassium iodine), for example in water or alcohol mixtures.PVP-iodine can in some examples include at least 1% polyvinylpyrrolidone(e.g., at least 2%, at least 5%, at least 10%, at least 20%, at least30%, or at least 35%, such as about 1-35% polyvinylpyrrolidone) and atleast 1% iodine (e.g., at least 2%, at least 5%, at least 10%, at least20%, at least 30%, or at least 35%, such as about 1%-35% iodine) inwater (e.g., see U.S. Pat. Nos. 2,739,922 and 3,898,326)

In one example, the container of the counterstain formulation includesfuchsin (such as carbol fuchsin or basic fuchsin), neutral red, and/orsafranin 0. In one example, the aqueous counterstain formulationincludes fuchsin at a concentration of at least 0.01%, at least 0.02%,at least 0.03%, at least 0.05%, at least 0.1%, at least 0.2%, at least0.3%, at least 0.4%, or at least 0.5%, such as from 0.02% to 0.50%. Inone example, the counterstain formulation includes neutral red at aconcentration of at least 0.01%, at least 0.02%, at least 0.03%, atleast 0.05%, at least 0.1%, at least 0.2%, at least 0.3%, at least 0.4%,or at least 0.5%, such as from 0.02% to 1%. In one example, thecounterstain formulation includes safranin 0 at concentration of atleast at 0.1%, such as at least at 0.2%, at least at 0.3%, at least at0.4%, at least at 0.5%, at least at 0.6%, at least at 0.7%, or at leastat 0.8%, such as 0.1% to 1% or 0.1% to 0.8% safranin 0. The counterstaincan be formulated in water, but in some examples may include 1%-20%ethanol or methanol.

In some examples, the containers or vessels that include the primarystain formulation, trapping agent formulation, slow-acting decolorizingagent formulation, and/or counterstain formulation, are configured orshaped for loading into automatic staining equipment. For example, thecontainers can be configured to be used with Ventana Medical Systems,Inc. equipment such as the NexES Special Stainer or a Ventana BenchMarkSpecial Stainer. In some examples, the containers are configured to beused with the Benchmark XT, Benchmark Ultra, or Discovery system, suchas those disclosed in U.S. Pat. No. 6,352,861, U.S. Pat. No. 5,654,200,U.S. Pat. No. 6,582,962, U.S. Pat. No. 6,296,809, and U.S. Pat. No.5,595,707, all of which are incorporated herein by reference. Additionalinformation concerning automated systems and methods also can be foundin PCT/US2009/067042, which is incorporated herein by reference. In oneexample, the container is a chemically resistantpolypropylene/polyethylene vial, such as a Ventana BenchMark dispenser.

The kits may also include one or more microscope slides, such as slidesuitable for mounting and in some examples fixing a sample, as well ascoverslips, pipettes, or combinations thereof.

The kit can optionally also include control slides for verifying thereagents and proper implementation of the Gram stain protocol. Forexample, one set of control slides can include Gram-positive bacteria,such as Staphylococcus aureus (or any of those listed herein), andanother set of control slides can include Gram-negative bacteria, suchas Escherichia coli (or any of those listed herein). In some examples, acontrol slide in the kit includes no bacteria.

The kit can optionally further include additional reagents forperforming additional assays. For example, the kit can include one ormore vessels or containers that contain other dyes or stains, such ascontainers that include one or more of the following stains: Acid FastBacilli (AFB) III, Alcian Blue, Alcian Blue for Periodic Acid Schiff(PAS), Alcian Yellow, Congo Red, Diastase, Elastic, Giemsa, Grocott'sMethenamine Silver stain (GMS) II, iron, Jones Light Green, Jones, LightGreen for PAS, Mucicamine PAS, Reticulum, Steiner II, Trichrome Blue,and Trichrome Green. In one example, the kit can include a vessel orcontainer that contains bacteria-specific antibodies. In some examples,the kit includes a vessel or container that contains labeled secondaryantibodies (e.g., labeled with a fluorophore or quantum dot).

Slow-Acting Decolorizing Compositions

The disclosure also provides slow-acting decolorizing formulations thatcan be used in the kits and methods provided herein. In one example, theslow-acting decolorizing formulation includes a mixture of both aslow-acting decolorizing agent, and a fast-acting decolorizing agent,such as one or more slow-acting decolorizing agents and one or morefast-acting decolorizing agents.

In one example, the slow-acting decolorizing formulation includes one ormore slow-acting decolorizing agents, such as at least 80%, at least81%, at least 82%, at least 83%, at least 84%, at least 85%, at least86%, at least 87%, at least 88%, at least 89%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99%, or at least 99.9% of oneor more slow-acting decolorizing agents (e.g., 1,2-propanediol, ethyleneglycol, or combinations thereof), such as 80% to 99.99% of one or moreslow-acting decolorizing agents. In one example, the slow-actingdecolorizing formulation includes one or more fast-acting decolorizingagents, such as no more than 20%, no more than 19%, no more than 18%, nomore than 17%, no more than 16%, no more than 15%, no more than 14%, nomore than 13%, no more than 12%, no more than 11%, no more than 10%, nomore than 9%, no more than 8%, no more than 7%, no more than 6%, no morethan 5%, no more than 4%, no more than 3%, no more than 2%, no more than1%, no more than 0.5%, or no more than 0.01% of one or more fast-actingdecolorizing agents (e.g., propyleneglycol methyl ether, diethyl ether,ethanol, acetone, methanol, 1-propanol, 2-propanol, 1-butanol, orcombinations thereof, such as blends of ethyl alcohol and acetone andblends of ethyl alcohol with other alcohols such as methanol or2-propanol), such as 0.01% to 20%, 0.1% to 20%, 0.1% to 10%, 1% to 20%,or 1% to 10%, of a fast-acting decolorizing agent.

Example 1 Comparison of Gram Staining Decolorizing Agents

This example describes methods used to compare decolorizing agents inGram staining in order to optimize the rate of decolorization. CrystalViolet and Gram Iodine were prepared according to the procedure ofCarson F, Hladik C. Histotechnology: A Self Instructional Text, 3rdedition, pp. 231-233. Hong Kong: American Society for Clinical PathologyPress; 2009 (incorporated herein as reference).

Paraffin embedded tissue sections of Gram-positive controls weredeparaffinized using standard histological techniques. These were thenstained on an automated prototype stainer in which the crystal violetwas dispensed dropwise (˜90 μL per drop) on the horizontally positionedtissue section, allowed to incubate for approximately 4 minutes, andthen rinsed with an aqueous surfactant solution. Gram iodine was thenapplied dropwise to the section and this was incubated for about 4minutes followed by rinsing. At this point, the decolorizing solvent wasadded to the tissue section manually using a calibrated pipette,followed by manually rinsing with the aqueous surfactant solution atspecified time periods. A counterstain of Carbol Fuchsin and Tartrazinewas then applied manually (90 and 15 sec incubations, respectively). Theslides were then dehydrated and cleared to xylenes, followed bycoverslipping with permanent mounting media. Examination under amicroscope (20-200×) enabled evaluation of the selectivity of thesolvent for decolorizing the Gram (-) bacteria. The results are shown inthe table below.

Solvent Type Incubation time Result* 1,2-propanediol (PG) invention 210sec  +/0 1,2-propanediol (PG) invention 60 sec + 1,2-propanediol (PG)invention 30 sec + 50% PG/50% invention 57 sec 0 propyleneglycol methylether 50% PG/50% invention 74 sec 0 propyleneglycol methyl ether 80%PG/20% invention 74 sec + propyleneglycol methyl ether 2-propanolcomparative 20 sec − *+ = Gram (−) are red, Gram (+) are blue; 0 = minordecolorization of Gram (+); − = gram (+) bacteria decolorized

In view of the many possible embodiments to which the principles of thedisclosure may be applied, it should be recognized that the illustratedembodiment is only an example of the disclosure and should not be takenas limiting the scope of the invention. Rather, the scope of thedisclosure is defined by the following claims. We therefore claim as ourinvention all that comes within the scope and spirit of these claims.

We claim:
 1. A kit for automated Gram staining comprising: a slow-actingdecolorizing formulation in a first container.
 2. The kit of claim 1,further comprising: a primary stain formulation in a second container atrapping agent formulation in a third container; and a counterstainformulation in a fourth container.
 3. The kit of claim 2, wherein thefirst container, second container, third container and fourth containeris configured for loading into automated staining equipment.
 4. The kitof claim 1, further comprising one or more microscope slides.
 5. The kitof claim 1, further comprising one or more control slides.
 6. The kit ofclaim 2, wherein the contents of the first container, second container,third container and fourth container are used to contact a sample in thefollowing order: second container, third container, first container,fourth container; wherein the contents of two containers can be used atthe same time.
 7. The kit of claim 1, wherein the slow-actingdecolorizing formulation comprises 1,2-propanediol or ethylene glycol.8. The kit of claim 1, wherein the slow-acting decolorizing formulationcomprises a mixture of 1,2-propanediol and ethylene glycol.
 9. The kitof claim 1, wherein the slow-acting decolorizing formulation comprises aslow-acting decolorizing agent and a fast-acting decolorizing agent. 10.The kit of claim 9, wherein the slow-acting decolorizing formulationcomprises at least 80% of the slow-acting decolorizing agent and no morethan 20% of the fast acting decolorizing agent.
 11. The kit of claim 2,wherein the primary stain formulation comprises crystal violet orGentian violet.
 12. The kit of claim 11, wherein the primary stainformulation further comprises ammonium oxalate.
 13. The kit of claim 11,wherein the primary stain formulation further comprises isopropanol,ethanol, and methanol.
 14. The kit of claim 2, wherein the trappingagent formulation comprises iodine.
 15. The kit of claim 14, wherein thetrapping agent formulation further comprises water or alcohol.
 16. Thekit of claim 2, wherein the counterstain formulation comprises fuchsin,neutral red, and/or safranin O.
 17. The kit of claim 16, wherein thecounterstain formulation further comprises water.
 18. The kit of claim16, wherein the counterstain formulation further comprises tartrazine19. The kit of claim 16, wherein the fuchsin is basic fuchsin.
 20. Thekit of claim 16, wherein the counterstain formulation comprises fuchsinat a concentration of at least 0.1%.